DUF1284 - PFAM28P - GREMLIN Contacts

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DUF1284 - Protein of unknown function (DUF1284)

PFAM:	PF06935	Sequences: GYSPEFVENMTRIVERLRAGPDTPIELVEGPDDICAPCPNKEGHCGSEEKVRERDRAVLELLGLKPGERLTWDELLERIREKIFPEGWLREICGGCEWLELC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (102)
Sequences:	2093 (1707)
Seq/√Len:	169.0
META:	0.766

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_E	69_R	5.219	1.00
48_E	52_R	3.703	1.00
24_P	69_R	2.899	1.00
72_W	76_L	2.633	1.00
78_R	82_K	2.611	1.00
29_E	66_P	2.501	1.00
22_D	73_D	2.359	1.00
65_K	68_E	2.260	1.00
71_T	74_E	2.233	1.00
89_L	99_L	2.199	1.00
47_S	50_K	2.193	1.00
31_P	41_K	2.075	1.00
70_L	75_L	1.895	1.00
4_P	8_E	1.717	1.00
14_V	18_R	1.682	1.00
58_V	61_L	1.640	1.00
27_L	64_L	1.601	1.00
29_E	56_R	1.520	1.00
31_P	54_R	1.512	1.00
63_G	82_K	1.493	1.00
77_E	81_E	1.421	1.00
50_K	54_R	1.418	1.00
9_N	62_L	1.407	1.00
57_A	60_E	1.392	1.00
16_R	23_T	1.380	1.00
17_L	72_W	1.365	1.00
53_E	57_A	1.343	1.00
31_P	44_H	1.340	1.00
54_R	92_I	1.339	1.00
84_F	87_G	1.339	1.00
10_M	34_I	1.325	1.00
57_A	61_L	1.308	1.00
5_E	37_P	1.296	1.00
83_I	92_I	1.283	1.00
59_L	64_L	1.271	1.00
13_I	34_I	1.245	1.00
56_R	60_E	1.245	1.00
58_V	92_I	1.236	1.00
50_K	97_E	1.204	1.00
29_E	59_L	1.154	1.00
36_A	77_E	1.114	1.00
24_P	71_T	1.069	1.00
9_N	33_D	1.061	0.99
9_N	13_I	1.042	0.99
44_H	48_E	1.042	0.99
52_R	60_E	1.035	0.99
90_R	99_L	1.016	0.99
53_E	56_R	0.995	0.99
51_V	54_R	0.993	0.99
15_E	19_A	0.985	0.99
47_S	54_R	0.985	0.99
33_D	36_A	0.981	0.99
83_I	87_G	0.953	0.99
13_I	33_D	0.927	0.99
2_Y	6_F	0.910	0.98
26_E	67_G	0.903	0.98
12_R	15_E	0.899	0.98
53_E	95_G	0.893	0.98
48_E	51_V	0.875	0.98
10_M	14_V	0.869	0.98
22_D	69_R	0.867	0.98
61_L	92_I	0.866	0.98
89_L	92_I	0.864	0.98
97_E	101_L	0.859	0.98
54_R	83_I	0.857	0.98
85_P	102_C	0.856	0.98
84_F	90_R	0.852	0.98
38_C	43_G	0.852	0.98
4_P	7_V	0.838	0.97
76_L	80_R	0.821	0.97
1_G	6_F	0.816	0.97
1_G	10_M	0.808	0.97
40_N	47_S	0.806	0.97
11_T	34_I	0.804	0.97
80_R	102_C	0.801	0.97
16_R	20_G	0.799	0.96
46_G	52_R	0.797	0.96
64_L	70_L	0.794	0.96
67_G	70_L	0.773	0.96
57_A	91_E	0.760	0.95
16_R	19_A	0.759	0.95
82_K	88_W	0.757	0.95
61_L	88_W	0.754	0.95
62_L	78_R	0.752	0.95
21_P	73_D	0.749	0.95
47_S	79_I	0.749	0.95
90_R	95_G	0.741	0.95
40_N	46_G	0.738	0.95
9_N	34_I	0.732	0.94
75_L	87_G	0.712	0.93
48_E	95_G	0.711	0.93
9_N	37_P	0.708	0.93
30_G	46_G	0.700	0.93
93_C	96_C	0.693	0.92
54_R	101_L	0.691	0.92
80_R	85_P	0.684	0.92
11_T	15_E	0.682	0.92
48_E	54_R	0.675	0.91
12_R	19_A	0.663	0.91
25_I	75_L	0.663	0.91
46_G	49_E	0.657	0.90
15_E	18_R	0.653	0.90
41_K	44_H	0.652	0.90
18_R	73_D	0.646	0.90
97_E	100_E	0.643	0.89
68_E	71_T	0.642	0.89
20_G	23_T	0.636	0.89
9_N	12_R	0.625	0.88
1_G	7_V	0.619	0.88
87_G	99_L	0.618	0.87
10_M	39_P	0.617	0.87
29_E	52_R	0.614	0.87
54_R	58_V	0.610	0.87
62_L	84_F	0.606	0.86
38_C	41_K	0.605	0.86
69_R	75_L	0.601	0.86
72_W	83_I	0.599	0.86
7_V	10_M	0.595	0.85
16_R	21_P	0.594	0.85
28_V	33_D	0.587	0.85
15_E	22_D	0.585	0.85
72_W	80_R	0.584	0.84
22_D	71_T	0.584	0.84
90_R	102_C	0.583	0.84
51_V	58_V	0.582	0.84
65_K	74_E	0.581	0.84
14_V	72_W	0.578	0.84
32_D	96_C	0.575	0.83
18_R	77_E	0.572	0.83
49_E	53_E	0.568	0.83
15_E	42_E	0.566	0.83
85_P	89_L	0.563	0.82
16_R	33_D	0.558	0.82
2_Y	98_W	0.557	0.82
59_L	68_E	0.552	0.81
84_F	102_C	0.551	0.81
89_L	102_C	0.550	0.81
84_F	88_W	0.549	0.81
20_G	61_L	0.526	0.78
78_R	83_I	0.525	0.78
76_L	79_I	0.525	0.78
71_T	100_E	0.523	0.77
3_S	75_L	0.521	0.77
46_G	65_K	0.519	0.77
83_I	101_L	0.519	0.77
61_L	91_E	0.517	0.77
62_L	102_C	0.517	0.77
91_E	94_G	0.515	0.76
51_V	94_G	0.510	0.76
10_M	17_L	0.508	0.75
62_L	99_L	0.507	0.75
56_R	66_P	0.504	0.75
10_M	18_R	0.500	0.74

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3u4qB	1	0.6275	24	0.889	Contact Map
3idwA	1	0.4608	20.3	0.893	Contact Map
2xu0A	1	0.5294	17.7	0.896	Contact Map
2yk0A	1	0.9706	4.8	0.92	Contact Map
1ylfA	5	0.5784	4.5	0.92	Contact Map
4ic1A	5	0.4314	4.3	0.921	Contact Map
2hw4A	1	0.3039	3.9	0.923	Contact Map
2nmmA	3	0.3039	3.8	0.923	Contact Map
4nrdA	3	0.8235	3.8	0.924	Contact Map
1uwvA	1	0.6667	3.5	0.925	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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